INTERNATIONAL PHD PROGRAM FELLOWSHIPS BSC LA CAIXA 2016

Closing Date: Monday, 29 February, 2016

Since 1982, the “la Caixa” Foundation has offered several fellowship programmes aimed at allowing students to undertake postgraduate studies in Spain and abroad. Over the years, thousands of students have advanced their training thanks to a “la Caixa” Foundation fellowship. In 2008, the “la Caixa Foundation launched a new programmed aimed at national and international students. As part of this programme, each year fellowships are awarded to students who wish to complete work toward their doctoral degrees.

BSC-CNS is at the service of the international scientific community and industry that require High Performance Computing resources. The multidisciplinary research team and the computational facilities –including MareNostrum – make BSC-CNS an international center of excellence in e-Science.

Under a collaborative Framework Agreement, the Ministry of Economy and Competitiveness and the “la Caixa” Foundation continue the fellowship programme with a 3rd call. This programme aims to help the recruitment of talented students from across the world by doing their doctoral thesis work in one of the accredited “Severo Ochoa” centers of excellence. The objective of this joint activity is to boost the research capacity of the best research institutions in Spain. For this year, the “la Caixa” Foundation has selected the Barcelona Supercomputing Center (BSC-CNS) to offer 2 grants more for the academic year 2016-2017 addressed to PhD students. This grant is renewable up to four years.
BSC-CNS is looking for young scientists from the national and international community. We encourage applications from highly motivated engineers and computational scientists with outstanding qualifications. Successful candidates will join research groups with top-level scientists and will carry out their research in cutting-edge areas of Computer Sciences, Life Sciences, Earth Sciences and Computer Applications in Sciences and Engineering

Conditions and benefits

The training programme will last 4 years to complete the PhD thesis. It’s offered an internationally competitive salary.
BSC-"la Caixa" fellows will benefit from the Training Programme and BSC staff benefits:

• International multidisciplinary scientific environment.
  

• Advanced research training
  

• Advanced computational facilities
  

Requirements:

The programme is addressed to all Master students (european and international) who have completed one of the following options by September 2016:

1. Studies that lead to an official Spanish (or from another country of European higher Education Area) university master degree in Computer Sciences, Biology, Chemistry, Physics, Environmental Sciences or related areas and that have 300 credits (ECTS) of an official university degree, of which at least 60 must correspond to master level.
   
   

1. Degree in a non-Spanish university not adapted to the European Higher Education Area with access to doctoral studies in Computer Sciences, Biology, Biochemistry, Physics, Environmental Sciences or related areas.
   

Applicants should not be PhD students at BSC-CNS. Candidates are selected exclusively on merit, on the basis of their curricula. The academic grades and curricula of applicants are evaluated, as well as recommendation and motivation letters. No selection criteria for positive or negative discrimination are applied.

Skills Specifications:

• Ability to take initiative, prioritize and work under set deadlines and pressure
  

• Ability to work independently and in a team
  

• Excellent written and verbal communication skills
  

• High level of English.
  

• Skills in programming
  

Interested candidates, please submit:

• Curriculum vitae
  

• A motivation letter
  

• A scanned copy of the student’s certified Academic Record. These documents must show the grades attained in exam periods.
  

• Two recommendation letters from university lecturers or scientists with who the applicant has studied or worked.
  

• Any additional files considered relevant to the application
  

Students will be required to provide a brief summary of work experience and to request letters of recommendation from two scientists who are familiar with their academic work and who can judge their potential as a PhD student. Only letters with official letterhead and signature will be accepted.
Applicants must indicate in the application form up to one research programmes in which they would like to work, in order of preference. Moreover, if candidates have interest in a particular research group, they must indicate it in the applications form and they should mention it in the cover letter. More information on the research activities of each group can be found on the BSC-CNS web pages.
Applicants must submit information in English (CV, motivation letter, summary of work experience). If the certified academic records are not in Catalan, Spanish or English applicants should also attach a sworn translation in one of the above mentioned languages.

Selection procedure

Students are selected from a pool of highly qualified international applicants on the basis of academic and technical excellence.

Applicants who have not been successful but have received a positive evaluation will be put on a waiting list to cover possible renunciations and other PhD fellowships in the center.

December 23th     Call Opening

February 29th       Call Deadline

March 1-April 6   Pre-selection of Candidates and documentation correction 

April 7-9               First Resolution

April 6-April 22    First Interviews 

April 23-25           Second Resolution

may-18                 Final Interviews and presentation with Recruitment Committee  

May 25-31           Final Resolution 

Sept/Oct 2016      Start date of fellowships

Apply Online 

PhD in Plant Pathology in the Plant Pathology group at the ETH Zurich

A PhD position is available in the Plant Pathology group at the ETH Zurich. The candidate will develop a research project to evaluate the molecular mechanisms controlling the effect of multi-infections on disease development in plants and pathogen evolution.
 

Summary of project

Natural infections are often caused by mixtures of genetically different pathogen strains (multi-infection). The consequences of simultaneous infection by multiple pathogen strains on disease development, epidemiology and pathogen evolution remain largely unexplored. This research project aims to understand the consequences of multi-infections on disease outcome and pathogen evolution.
 
Zymoseptoria tritici (also called Mycosphaerella graminicola) is a major fungal pathogen of wheat that commonly exhibits multi-infection in nature. Extensive knowledge of Z. tritici population genetics and genomics, transcriptomics and infection processes already exist, and advanced quantitative measures of virulence based on digital image analysis have already been developed. Hence Z. tritici provides a powerful model system for studying the consequences of multi-infections.
 
This research project has three main objectives:

1- Determine the effect of multi-infections on disease development and epidemiology.
2- Characterize how growth patterns in planta are affected in multi-infections compared to mono-infections.
3- Characterize the molecular mechanisms underlying strain interactions in multi-infections.
 

Supervisors: Dr. Andrea Sanchez Vallet, Prof. Bruce A. McDonald

 
Requirements: We seek highly motivated individuals interested in host-parasite interactions. Experience in molecular biology, confocal microscopy and bioinformatics is preferred, but not required. Requirements include a BSc or MSc in plant science, microbiology or plant pathology and good spoken and written English.
 
Group: The Professorship of Plant Pathology conducts research related to the molecular biology, population genomics and evolutionary ecology of plant pathogens. It is embedded within the Institute of Integrative Biology at the ETH Zurich, which possesses advanced research infrastructure including the Genetic Diversity Center and the Functional Genomics Center.
 
Applications:  The application should include a 2-3 pages motivation letter describing your research interests and your rationale for applying for this PhD position, a detailed CV that includes all relevant experience, and names, addresses and phone numbers of three referees. The application should be submitted as a single pdf file sent to andrea.sanchez@usys.ethz.ch before the 15^th February.

PhD studentships on the ERC project Skye: A programming language bridging theory and practice for scientific data curation , University of Edinburgh

Project description

Science is increasingly data-driven. Scientific research funders now routinely mandate open publication of publicly-funded research data. Safely reusing such data currently requires labour-intensive curation. Provenance recording the history and derivation of the data is critical to reaping the benefits and avoiding the pitfalls of data sharing. There are hundreds of curated scientific databases in biomedicine that need fine-grained provenance; one important example is the IUPHAR/BPS Guide to Pharmacology database (GtoPdb), a pharmacological database developed in Edinburgh.
Currently there are no reusable methodologies or practical tools that support provenance for curated databases, forcing each project to start from scratch. Research on provenance for scientific databases is still at an early stage, and prototypes have so far proven challenging to deploy or evaluate in the field. Also, most techniques to date focus on provenance within a single database, but this is only part of the problem: real solutions will have to integrate database provenance with the multiple tiers of web applications, and no-one has begun to address this challenge.
The Skye project will build support for curation into the programming language itself, building on recent research on the Links Web programming language, including advances in language-integrated query, and on provenance and data curation. Links is a strongly-typed language that provides state-of-the-art support for language-integrated query and Web programming. This project will build on Links and other recent language designs for heterogeneous meta-programming to develop a new language, called Skye, that can express modular, reusable curation and provenance techniques. To keep focus on the real needs of scientific databases, Skye will be evaluated in the context of GtoPdb and other scientific database projects. Bridging the gap between curation research and the practices of scientific database curators will catalyse a virtuous cycle that will increase the pace of breakthrough results from data-driven science.
Skye will draw on the best ideas developed in cutting-edge research on language-integrated query, Web programming, and heterogeneous meta-programming. Skye will provide dialects, or first-class client language definitions, along with translations that map programs written in one dialect to another, or (as a special case) that perform source-to-source translation on a single dialect, for optimisation or to add functionality such as provenance- tracking. These translations will be available as libraries that can change the behaviour of already-written applications by rewriting code, so scientific database developers using Skye will be able to reuse these features instead of having to reimplement them from scratch or make wholesale changes to existing applications.
The Skye project will support a group of PhD students and postdoctoral researchers under the leadership of Dr. Cheney to pursue research on programming language design for integrating Web programming and databases, in aid of scientific data management. Topics for research could include:

• Language design: How can we program with first-class client languages (dialects) and translations flexibly and safely?
• Expressing and optimising client languages: How can existing client languages be embedded as dialects and translated to efficient client language code?
• Defining modular curation techniques: How can existing (or new) curation techniques be defined using type-safe translations among dialects?
• Case studies: What are the benefits and costs of using Skye to develop curated scientific databases?

For additional information about the project background, please consult our recent publications on this subject here and here.

PhD studentships

Two 4-year PhD studentships will be supported by the project. One studentship will cover full fees and a stipend of approximately £14,000 per year for a student of any nationality and the other will cover fees and stipend for a student with UK or EU citizenship. Additional funding may be available for exceptional candidates.

Background required

Both PhD studentships will carry out fundamental research relevant to the project. It is anticipated that one student will be recruited in 2016 (preferably with a project focusing on web and database programming language design and implementation) and the other in 2017 (preferably with a project focusing on data curation and applications of Skye).
Accordingly, we are currently seeking applicants with a strong background and research interests in functional programming, typed language design and implementation, metaprogramming, or Web/database programming. Candidates with demonstrated research ability in programming languages, and with at least some familiarity with databases or bioinformatics, would be especially suitable for this project. Outstanding candidates with a database-centric background and some familiarity with programming languages research will also be considered at this stage.

About the position

This PhD studentship provides a total of 4 years funding for full-time research (with no required teaching obligations). This can be structured as a 4-year PhD (for candidates who already have research experience e.g. a suitable Master's project) or as a 1-year Master's by Research followed by 3 years of PhD research, hosted in one of the School's two EPSRC Centres for Doctoral Training, in Data Science or Pervasive Parallelism. Prospective applicants are encouraged to discuss these alternatives with the supervisor before applying.

Application information

To apply, please follow the instructions here. Please make sure to indicate interest in this project as part of the application.

Source

Postdoctoral position on graph databases and provenance management, University of Edinburgh

Project:	ADAPT: A Diagnostics Approach for Persistent Threat Detection
Supervisor:	James Cheney
Deadline:	February 12, 2015, 5pm GMT

We have an opening for a Research Associate in Graph Data Management on the project "ADAPT: A Diagnostics Approach to Advanced Persistent Threat Prevention", part of the "Transparent Computing" programme funded by the US Defence Advanced Research Projects Agency (DARPA).

Project description

"ADAPT: A Diagnostics Approach to Advanced Persistent Threat Prevention", is part of the "Transparent Computing" programme funded by the US Defence Advanced Research Projects Agency (DARPA). Transparent Computing (TC) is a $60 million research initiative to use provenance to improve security of critical systems in the face of advanced persistent threats (APTs), or attackers who gradually infiltrate a system in order to achieve long-term (and often highly damaging) objectives.

ADAPT is one of several TC-funded research projects working together to instrument mainstream systems to collect provenance, manage and analyse the resulting massive amounts of provenance graph data, and diagnose or identify potential attacks and attackers. ADAPT is a joint project between Galois Inc., Xerox PARC, Oregon State University, and the University of Edinburgh. The University of Edinburgh team is focusing on applying provenance and database expertise to support provenance graph queries and segmentation/feature extraction, needed by normalcy detection, classification, and diagnosis techniques provided by the other ADAPT partners.

About the position

This position is based at The University of Edinburgh. You are expected to take a leading role in investigating graph database techniques applied to provenance management problems in the ADAPT project. In particular, you are expected to play an important role in leading to the successful completion of one or more of the following project tasks:

• Specify and implement techniques for identifying segments or features in provenance graphs
• Analyse and improve the performance of such queries or extraction techniques on large-scale provenance graph data
• If necessary, develop new query language features or optimizations tailored to the provenance graph queries needed by other parts of the project
• Investigate incremental or stream-based techniques for extracting needed data from provenance graphs
• Develop and implement abstractions for hierarchical modelling and causal linking of activities in provenance graphs, as needed by other parts of the project

The position will require system development as part of an international research project, as well as independent ideas-led research. You will be expected to work effectively with other researchers to produce prototypes, production-quality systems, high quality publications and demonstrations, and contribute to dissemination activities for the project, e.g. participating in project meetings and publishing papers in top conferences and journals. Duties will also include intermittent travel to project meetings.

Background required

The successful candidate will have expertise in databases, particularly graph data management, provenance management, query languages and optimisation, or incremental computation. The emphasis of this position is on systems-oriented research and development, so experience with database systems implementation is essential; programming languages preferred for the project include Haskell, Scala, and Python. Familiarity with virtualization technology (Docker), message queues (Apache Kafka), graph databases (Titan/Cassandra; Gremlin), or provenance querying and standards (e.g. W3C PROV) would be especially advantageous.
Applicants must, at a minimum, have a PhD degree (or be close to completion) in Computer Science, with either a track record of high quality publications or industrial experience adequate to the needs of the project. A strong background in graph databases/systems (or the ability to learn new systems quickly) is required. We expect that the project will involve practical systems development informed by conceptual or foundational research, so an ideal candidate will have strong development skills and the ability to engage with theory. Previous research experience on provenance or related topics such as machine learning/classification and information flow security would be desirable.
Please ensure that your application includes:

• a CV listing relevant education, research experience and publications.
• a 1-2 page statement of your research interests and how they relate to this position.

Applications that do not include these documents may not receive full consideration.

Duration and starting date

The postdoctoral position is available for 18 months starting on or as soon as possible after March 1, 2016.

The Transparent Computing programme as a whole will run from July 2015 until June 2019. This postdoctoral position is subject to extension beyond the initial 18 months, contingent on availability of funding.

Prospective applicants are encouraged to contact James Cheney (jcheney@inf.ed.ac.uk) before applying to discuss the position.

Application process and deadlines

A complete application consists of a CV and a 1-2 page research statement summarizing your background, previous research experience, and how they relate to this position.

Applications must be submitted by 5pm GMT on February 12, 2016, through the University of Edinburgh recruitment site:
https://www.vacancies.ed.ac.uk
Reference number: 035230
or directly by following this link:
direct link to the application site
Interviews will likely be held (either in person or via Skype) in mid-February.

Source